I spent a couple days playing with solid state drives (USB, compactflash, and 2.5in SSD), and discovered a number of things:

File systems:
-exFAT may provide slightly better performance on some USB drives, but it has poor compatibility (tried it on my Snow Leopard MacBook: no go; the Paragon Alignment Tool I used also tended to be unable to align exFAT partitions)
-NTFS is best for stationary drives (ie, don’t bother using with removable flash if you are constantly plugging/unplugging)
-FAT16 (or just “FAT”) is only applicable for drives 4GB and under, otherwise same compatibility benefit as FAT32
-FAT32 was the go-to filesystem for removable flash, due to its wide compatibility and selection of allocation unit sizes

Allocation unit sizes:
-for data transfer, 64KB is the way to go (gives you the best sequential writes)
-for Readyboost, 4KB is the best size (4KB read is the most important spec for Readyboost)

Alignment:
Jury still out on this one, but I was able to shave around 0.3 seconds off my boot time of 22.9 seconds on a Kingston SSDnow V-series (gen2) with the Paragon Alignment Tool. I intentionally installed WinXP on the drive RAW to create a less-than-optimal alignment. I wasn’t expecting a less than 2% improvement, but this drive is known for it own aggressive internal optimizations, and not being particularly sensitive to alignment, so, I guess I’m not too surprised.

Readyboost:
-4K read seems to be the only spec that matters – use CrystalDiskMark to check your drive – if less than 3MB/s, its probably not worth being a Readyboost drive.
-as already mentioned, you want to set the allocation unit size to 4096 bytes (this means FAT16 is out)